Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome

Martin Krzywinski, John Wallis, Claudia Gösele, Ian Bosdet, Readman Chiu, Tina Graves, Oliver Hummel, Dan Layman, Carrie Mathewson, Natasja Wye, Baoli Zhu, Derek Albracht, Jennifer Asano, Sarah Barber, Mabel Brown-John, Susanna Chan, Steve Chand, Alison Cloutier, Jonathon Davito, Chris FjellTony Gaige, Detlev Ganten, Noreen Girn, Kurtis Guggenheimer, Heinz Himmelbauer, Thomas Kreitler, Stephen Leach, Darlene Lee, Hans Lehrach, Michael Mayo, Kelly Mead, Teika Olson, Pawan Pandoh, Anna Liisa Prabhu, Heesun Shin, Simone Tänzer, Jason Thompson, Miranda Tsai, Jason Walker, George Yang, Mandeep Sekhon, La Deana Hillier, Heike Zimdahl, Andre Marziali, Kazutoyo Osoegawa, Shaying Zhao, Asim Siddiqui, Pieter J. de Jong, Wes Warren, Elaine Mardis, John Douglas Mcpherson, Richard Wilson, Norbert Hübner, Steven Jones, Marco Marra, Jacqueline Schein

Research output: Contribution to journalReview article

31 Scopus citations

Abstract

As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide ∼13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

Original languageEnglish (US)
Pages (from-to)766-779
Number of pages14
JournalGenome Research
Volume14
Issue number4
DOIs
StatePublished - Apr 2004
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Fingerprint Dive into the research topics of 'Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome'. Together they form a unique fingerprint.

  • Cite this

    Krzywinski, M., Wallis, J., Gösele, C., Bosdet, I., Chiu, R., Graves, T., Hummel, O., Layman, D., Mathewson, C., Wye, N., Zhu, B., Albracht, D., Asano, J., Barber, S., Brown-John, M., Chan, S., Chand, S., Cloutier, A., Davito, J., ... Schein, J. (2004). Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Research, 14(4), 766-779. https://doi.org/10.1101/gr.2336604